Molecular mechanics (MM3) calculations on lithium amide compounds

The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations.     

Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives

The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics calculations (MM3) on sulfones

The structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6-31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on alkyl radicals

The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on azoxy compounds

The MM3 force field has been extended to include azoxy compounds and also the related amine oxides, both aliphatic and aromatic. The structures of nine molecules were all well fit. The heats of formation for the aliphatic compounds were also well fit, and the vibrational spectra of eight compounds were also fit to the accuracy expected for such calculations. Because many of the experimental data needed to derive the force field were either lacking or were inadequate, ab initio calculations on structures, optimized at the MP2/6-31G* level, were used as needed. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on conjugated hydrocarbons

The MM3 molecular mechanics program has been extended to conjugated systems. A VESCF method is applied to the pi-system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm^?1, and from these, other properties such as entropy can be calculated.     

Molecular mechanics calculations (MM3) on bicycloalkyl hydrocarbons

A series of bicycloalkyl hydrocarbons were studied using molecular mechanics methods (MM3), and the results were compared with the experimental data available. Five compounds were studied: bicyclopropyl, bicyclobutyl, bicyclopentyl, bicyclohexyl and 2,3-dimethylbutane. In general, the MM3 results are in good agreement with experimental values. Predicted structures and conformations are given for the bicyclopentyl previously uninvestigated experimentally.     

Molecular mechanics (MM4) study of amines

The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.     

A molecular mechanics (MM3) study of fluorinated hydrocarbons

A molecular mechanics study of small saturated hydrocarbons (up to C-6), substituted by up to six fluorines was carried out with the MM3 force field. Perfluorobutane and Teflon were also studied. A parameter set was developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia and vibrational frequencies for these compounds. The results are in good agreement with experiment when only one or two fluorines are present, but some rather large discrepancies were noted when the F/H ratio becomes high. These can be taken into account only by using a force field more complicated than MM3. Some of the requirements of such a force field are delineated. Some pertinent ab initio results are also reported in this article.     

Molecular mechanics studies (MM4) of sulfides and mercaptans

The MM4 force field has been extended to the title class of compounds. The vibrational spectra, structures, conformational equilibria, and heats of formation have been studied for 47 conformers of 29 compounds. In general, the properties may be calculated with accuracy that is competitive with that for hydrocarbons. The structures are better fit than previously because of the inclusion of a torsion–bend interaction term, which has its origin in the lone pair (Bohlmann) effect. Available experimental data do not suffice to yield detailed torsional potentials, or geometries as a function of torsion angle, and these quantities were determined by ab initio calculations at the MP2/6-31G* level. The rms error in the calculated frequencies of seven representative structures (with a total of 64 experimental and 96 ab initio frequencies) is 25 cm⁻¹. The heats of formation for 23 compounds have a weighted rms error of 0.36 kcal/mol. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1827–1847, 1997     

Molecular mechanics (MM3) parameterization for oxocarbenium ions

The physical properties of a diverse group of 12 oxocarbenium ions have been studied with ab initio calculations at the MP2/6‐31+G* level of theory. Based on theoretically derived properties such as molecular equilibrium geometry, dipole moment, and vibrational frequencies, a molecular mechanics (MM3) force field has been developed with the assistance of the programs TORSMART and MPMSR, components of our artificial parameter development and refinement method. The MM3 force field is now able to reproduce bond lengths, bond angles, moments of inertia, dipole moments, torsional energy profiles, and vibrational frequencies of oxocarbenium ions, which will allow further studies of glycoside hydrolysis and their rates of reaction. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 329–339, 2000     

Titanium(IV) terminal hydroxo complexes containing chelating bis(phosphine oxide) ligands

Treatment of [L_OEtTi(OTf)₃] (, OTf⁻ = triflate) with S-binapO₂ (binap = 2,2′-bis(diphenylphosphinoyl)-1,1′-binaphthyl) afforded the terminal hydroxo complex [L_OEtTi(S-binapO₂)(OH)][OTf]₂ (1). Treatment of [L_OEtTi(OTf)₃] with K(tpip) (tpip⁻ = [N(Ph₂PO)₂]⁻) afforded [L_OEtTi(tpip)(OTf)][OTf] (2) that reacted with CsOH to give [L_OEtTi(tpip)(OH)][OTf] (3). The structures of 1 and 2 have been determined.     

Stepwise phosphine sulfide formation and metal-bridging reaction of tetradentate and tridentate phosphine ligands on palladium(II)

Kinetic studies on the stepwise phosphine sulfide formation reaction of the five-coordinate trigonal-bipyramidal Pd(II) complexes with the tripodal tetradentate phosphine ligand, [PdCl(pp₃)]Cl and [Pd(4-Cltp)(pp₃)](BF₄) (pp₃ = tris[2-(diphenylphosphino)ethyl]phosphine; 4-Cltp = 4-chlorothiophenolate), were carried out, and it was revealed that the reactions proceeded via the intermediate with a pendant dissociated phosphino group. Formation of the intermediate was utilized for the bridging reaction onto Pt(II) to form the phosphine-bridged linear trinuclear and cyclic tetranuclear mixed-metal complexes. Difference in the steric conversion mechanism in the phosphine-bridging reaction between the linear tridentate phosphine (bis[2-(diphenylphosphino)ethyl]phenylphosphine) and pp₃ is also reported.     

Novel phosphine ligands bearing 3(5)-pyrazolyl and 4-(2-amino)pyrimidinyl groups: Synthesis and coordination chemistry

Novel triphenyl phosphine ligands bearing pyrazole or 2-aminopyrimidine groups in the ortho or meta position of one or three of the phenyl rings were obtained starting from the corresponding acyl derivatives Ph₂P(o-C₆H₄-COCH₃), Ph₂P(m-C₆H₄-COCH₃), or P(m-C₆H₄-COCH₃)₃. Conversion of the acyl groups into 3-dimethylamino-2-propen-1-onyl units was achieved by reaction with HC(OMe)₂NMe₂ which underwent ring closing with hydrazine or guanidine to yield the desired heterocycles. Two palladium complexes were synthesized using the coordinatively labile precursor (PhCN)₂PdCl₂, one of them could be characterized by X-ray structure analysis.     

Molecular mechanics (MM4) calculations on carbonyl compounds part I: aldehydes

Aliphatic aldehydes have been studied with the aid of the MM4 force field. The structures, moments of inertia, vibrational spectra, conformational energies, barriers to internal rotation, and dipole moments have been examined for six compounds (nine conformations). MM4 parameters have been developed to fit the indicated quantities to the wide variety of experimental data. Ab initio (MP2) and density functional theory (B3LYP) calculations have been used to augment and/or replace experimental data, as appropriate. Because more, and to some extent, better, data have become available since MM3 was developed, it was anticipated that the overall accuracy of the information calculated with MM4 would be better than with MM3. The best single measure of the overall accuracy of a force field is the accuracy to which the moments of inertia of a set of compounds (from microwave spectroscopy) can be reproduced. For all of the 20 moments (seven conformations) experimentally known for the aldehyde compounds, the MM4 rms error is 0.30%, while with MM3, the most accurate force field presently available, the rms error over the same set is 1.01%. The calculation of the vibrational spectra was also improved overall. For the four aldehydes that were fully analyzed (over a total of 78 frequencies), the rms errors with MM4 and MM3 are 18 and 38 cm^?1, respectively. These improvements came from several sources, but the major ones were separate parameters involving the carbonyl carbon for formaldehyde, the alkyl aldehydes and the ketones, and new crossterms featured in the MM4 force field that are not present in the MM3 version. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1396–1425, 2001     

Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205

The MM2 potential functions for amides and peptides have been further extended by examining the experimental crystal structures for cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), I, and cyclo-(-Ala-Ala-Gly-Ala-Gly-Gly-), II. The force field obtained was then applied to a study of the structure of the hydrophobic protein Crambin, for which a high resolution crystal structure is available. The energy minimization was carried out using a version of MM2 adapted to the CYBER 205.     

A molecular mechanics force field for rhodium(I) carbonyl phosphine complexes and its application on the oxidative addition reactions of these complexes

The main purpose of the development of an Rh(I) Carbonyl Phosphine force field was to predict the molecular structure of Rh(I) complexes as well as to compute possible intermediates or transition states during the oxidative addition of CH₃I to these complexes. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 692–703, 2000     

Experimental and theoretical characterization of Ru(II) complexes with polypyridine and phosphine ligands

The synthesis and the experimental and theoretical characterization of ruthenium hydride complexes containing phosphorus and polypyridine ligands [RuH(CO)(N-N)(PPh₃)₂]⁺ with N-N = dppz 1, dppz-CH₃2 (2.1 isomer), dppz-Cl 3 (3.1 isomer), ppl 4, and 2,2′-biquinoline 5, (where dppz = dipyrido[3,2-a:2′,3′-c]phenazine), are presented. ¹H NMR, ³¹P NMR, ¹³C NMR, IR-FT, UV-Vis and elemental analysis are used to characterize the complexes. Optimized molecular geometries in the gas phase at the B3LYP/LACVP(d,p) level showed a distorted octahedral structure for ruthenium, the phosphine ligands are localized in a trans position, while the polypyridine ligand, which in all the cases is planar except in 5, adopt a trans position relative to the carbon monoxide and hydride ligands. The theoretical absorption spectra (one hundred excited states) were calculated for the seven complexes by the time dependent density functional theory (TD-DFT) in the gas phase. They predicted very well the UV-Vis spectra. It was possible to identify the character of each electronic transition and the fragments of the complexes involved in it. Theoretical evidence of the substituent effect in the polypyridine ligand and of the ligand effect (dppz, biq, ppl) was found, displayed mainly in the longer wavelength band. The theoretical results showed that the properties of these complexes can be tuned with changes localized in the polypyridine ligand covalently bonded to ruthenium.     

Structural study of pyrimidine nucleoside analogues. I: Molecular mechanics and semiempirical calculations of 2′-deoxy-2′-fluoroarabinofuranosyluracils

Molecular mechanics (MM) calculations have been performed on the title compounds. For the MM minimum energy conformation obtained by conformational analysis, molecular orbital (MO) calculations (MNDO and AM1) have also been performed. The geometries obtained have been compared with the experimental ones extracted from the Cambridge Structural Database (CSD). A qualitative structure-activity relationship has been pointed out based on the electrostatic potentials calculated at different positions on the electronic surface.